MonoPhy

Explore Monophyly of Taxonomic Groups in a Phylogeny

R package to explore monophyly (or lack thereof) of taxonomic groups in a phylogenetic tree. Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc.Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways.

Usage instructions can be found in the manual and tutorial vignette. This is the developing branch, a stable version can be found on CRAN.

Citation:
Schwery, O. & O'Meara, B.C. (2016), MonoPhy: a simple R package to find and visualize monophyly issues. PeerJ Computer Science 2:e56. 10.7717/peerj-cs.56

_HexLogos made using hexSticker, integrated using usethis._